Knox/Sollecito: update on today’s court proceedings

July 30, 2011

Amanda Knox and Raffaele Sollecito

Photo by Franco Origlia

The prediction I made at the end of my last post that today’s hearing in the appeal of Amanda Knox and Raffaele Sollecito would be “the most enlightening and important session” in the process turned out a little wide of the mark, mainly because the meat of the prosecution response to the recent DNA review in the case didn’t happen. We will have to wait until after the court’s summer recess for that, when police scientist Patrizia Stefanoni will give evidence explaining why, in spite of the criticisms in the review, the DNA analysis she undertook in relation to two key pieces of evidence in the case is reliable.

That will be the most enlightening and important session in the process. Mark my words.

Today’s hearing began with the presentation in court of a letter from Stefanoni’s boss, Piero Angeloni, taking issue with the DNA review and affirming his confidence in the work of his people. It might be said that this tells us little we didn’t expect – after all, it already seemed clear that the police were not going to put up a white flag. Apart from support for Stefanoni, though, I think the real purpose of the letter to highlight how unusual the DNA review undertaken in the case is, in the view of the police. It is unprecedented, says Angeloni, for the police to be subjected to this type of criticism in court.

I wonder if this is a foretaste of a public policy argument the prosecution may seek to hang their hat on. The authors of the review, Stefano Conti and Carla Vecchiotti, start from a position of feeling they need to trawl through academic literature in order to piece together the standards by which they feel Stefanoni should have operated. But, it might be argued, this constitutes them assuming the role of a two-person regulatory body. Even if their recommendations are sound, it is the accepted regulatory framework that matters. The courts cannot permit the police to be subjected to creative criticism that goes beyond this framework because, in that case, the streets would quickly fill with acquitted murderers.

At least, I think that’s where we may be going, and it is also something that is reflected in what Stefanoni recently said to the Observer: “We followed the guidelines of the ENFSI, theirs is just a collage of different international opinions”.

Given what is said the review though, the question that immediately raises itself is how closely the ENFSI or any other guidelines have been followed. I don’t know what the standards required would have been on the relevant date, but it is likely that Stefanoni will need to convince the court that, for example, negative control tests were appropriately carried out on the samples taken from the alleged murder weapon. Arguing that you only need to follow certain agreed standards and then going on to argue that you don’t even need to follow those may be a step too far.

Meanwhile, each side seems to have scored a point in their cross-examination of the experts regarding that alleged murder weapon, a knife recovered by police from Raffaele Sollecito’s flat. The defence were able to elicit an opinion that the blade of the knife had been subjected only to a fairly ordinary wash prior to its discovery by the police. The judges will no doubt be wondering how likely it is that Knox and Sollecito dealt with their murder weapon by giving it only a general clean.

The prosecution, for their part, secured an agreement from Carla Vecchiotti that a six-day gap between the testing of the knife and any prior testing of items containing the DNA of Meredith Kercher would be sufficient to guard against contamination. This may be very helpful to prosecutors, since their main task is to show that the theoretical risks of contamination outlined in the DNA review could not have given rise to any actual contamination.

With respect to the other piece of evidence under consideration, the clasp from Kercher’s bra, said by prosecutors to bear Sollecito’s DNA, the most important answer may turn out to be one that wasn’t given. According to one report, when asked by prosecutor Manuela Comodi how it was possible that Sollecito’s DNA on the clasp could be the result of contamination, the two experts were not able to give any clearer explanation than “anything is possible”. That answer could well turn out to be an Achilles heal for the defence case.


Knox/Sollecito appeal hearing on 30th July

July 29, 2011

Barring delays, overruns or surprises, tomorrow should see the last hearing in the appeal of Amanda Knox and Raffale Sollecito before the court goes into summer recess.

On Monday, the court heard scientists Stefano Conti and Carla Vecchiotti give a rundown of their review of some of the DNA evidence in the case. They did this with the aid of a DVD containing crime scene footage, designed to illustrate flaws in police procedure in the collection and handling of evidence, but without being questioned by the prosecution or defence lawyers. This means that the likely points of contention in relation to the review have still not been gone into and, for information about that, I refer you to my previous posts here and here.

There have, however, been two developments reported in the Italian press which may stand some sort of chance of having some sort of impact on proceedings.

The Umbrialeft website is reporting that the above-mentioned DVD played to the court by Conti and Vecchiotti on Monday has since been subjected to a court order effectively stating that it forms part of the proceedings. The report is less than clear, though, as to why this event is newsworthy. My best attempt at inter-linear decoding says that what has gone on is that the prosecution have asked for a copy of the DVD and presiding judge Hellmann has then issued the order so that they might be entitled to a copy. This would just be an administrative tidying-up in relation to something that should really have been done during the court session.

However, I appreciate that this version is irritatingly probable and mundane, so here’s a different take. Francesco Maresca, lawyer for the family of Meredith Kercher, has recently been complaining to reporters that the DNA review does not appear to have been written from a disinterested standpoint. And, in last Sunday’s Observer, an unnamed police source went further, suggesting that the experts were being “fed information” by the defence.

Now, it’s all very well for lawyers and police officers to have suspicions about the integrity of the experts, but it’s not much use to the court without evidence. So, suppose that someone paying attention to DVD presentation on Monday noticed that it contained material which did not seem to have been supplied to the experts by the court. That might be prima facie evidence of undisclosed communication between the experts and the defence, or someone close to the defence. If those circumstances were to arise, the bench may well feel obliged to disregard the DNA review.

But let’s not get carried away. The simplest explanations are usually the best and, let’s face it, were the experts crooked they would surely not make such a basic error. Still, you never know…

Meanwhile, there has been a surprise twist regarding the evidence of Luciano Aviello, the gender-nonconformist Mafioso who testified a few weeks ago that the killer of Meredith Kercher was in fact his fugitive brother. At the time, this was more or less as obvious a lie as it is possible to imagine, particularly given Aviello’s record of eight separate convictions for criminal defamation and the fact that the court heard another witness claiming that Aviello had been offered a large some of money by the defence in return for his false testimony.

So, in the face of a police investigation into this claim, Aviello now says that he was offered €30,000 (which he intended to spend on a sex change operation) by the Sollecito family and with the knowledge of defence lawyers. Quite a price-tag for the worthless garbage they got in return, but maybe the Sollecitos have better money than judgement. What is more, Aviello now claims that Sollecito confided to him in prison that Knox, but not he, was responsible for the murder.

The main reason this is unlikely to have a major impact on the appeal is that, in the absence of corroborating evidence, Aviello is clearly no more reliable as a witness than he was a couple of weeks ago. The court will need to take account that his original tale, obviously and plainly false in any case, has now progressed to being plainly and obviously false. Prosecutors will need to decide whether it is worth pressing for him to testify again. Given that there exist more credible allegations as to the dirty hands of the Sollecito family, they may wish to add pressure on the bench to wonder if there might be an iceberg below. On the other hand, they may feel that the judges and juror-judges already have the information they need, and that it would be a mistake to draw attention away from the much more important matter of their rebuttal to the DNA review.

As a side-note, something that seems clear from the reporting of this story is that Aviello and Sollecito associated with each other in prison, at least according to Aviello. But, as far as I can tell, this rather material bit of information was not mentioned in court when Aviello testified on 18 June. Surely this is something that must have been known to the defence?

Regardless of whether any of these side-stories make it into the courtroom tomorrow, it promises to be the most enlightening and important session in the whole appeal. It won’t be possible to tell immediately whether it has been decisive but, for the prosecution, a lot hangs on how convincing or unconvincing their response to the DNA review turns out to be.


Knox/Sollecito DNA showdown: an overview (part two)

July 22, 2011

This is a continuation of the previous post.

Questions for the court

1. How certain are Conti and Vecchiotti of their conclusions?

Francesco Maresca, lawyer for the Kercher family, has made clear his view that the DNA review is simply too unequivocal. Whereas it might have weighed up various differing viewpoints and given indications of the relative strengths of different arguments, it is instead content to give a rather bald and linear opinion. Prosecutors will undoubtedly be hoping that greater acknowledgement of the complexities of DNA analysis can be extracted from Conti and Vecchiotti during questioning.

It may be a struggle to get them to cast doubt on the central threads of their own arguments. But maybe they will be willing to give way to the prosecution case on certain details. For example, one thing they suggest is that the bra-clasp might have become contaminated with Sollecito’s DNA because it hitched a ride on air-born dust. It might be felt that it would not be too big a deal for them to agree that this is, in reality, just as speculative as it sounds.

Getting concessions on those sorts of apparently minor details could do a lot to aid the prosecution case in two ways. Firstly, the logic contained in the DNA review might thereby be eroded. What’s more, from a tactical point of view, it can’t hurt to have its authors agreeing that there is more to what they say than meets the eye, even if that is something that can only be achieved on the fringes.

2. How clean was the lab?

If the prosecution can’t bring a convincing argument that the procedural standards in the laboratory where the DNA tests were carried out, then it may be that the court will lose confidence in the proposition that the knife can be considered to have been used in the crime.

The lab was preparing for ISO 9001 accreditation at the time when the tests were carried out. This may be significant, because that process included the development of internal process auditing. In other words, it may be that an audit report exists which will give a description of how analytical tasks were carried out in the lab at around that time. If so, then that document may well be able to tell the court everything it needs to know in order to determine the reliability of the testing carried out on the knife blade.

Whether such a report exists in reality and whether it will be entered as evidence is, of course, unknown.

What is also unknown is where things stand if, as may well turn out to be the case, the court has only the word of police scientist Patrizia Stefanoni or other people connected to the lab. Is it then just a question of the court’s credulity?

3. Where are the controls?

Conti and Vecchiotti say they can find no evidence that appropriate control experiments were run in tandem with the DNA testing on the knife so as to help ensure its reliability. In particular a negative control (i.e. running a “blank” test and checking that the results turned out blank) could have provided some evidence against the possibility of contamination.

If such controls were not carried out, is there any way in which this is defensible? If controls were carried out and were satisfactory but not recorded, is that good enough?

4. When is a stutter not one?

The DNA review employs simple but strict and inflexible mathematics in order to make distinctions between peaks in DNA printouts which should be considered stutters (meaningless noise) and those which should be considered genuine parts of the DNA information produced. For each peak, there is a height threshold, above which it should be considered genuine and below which it should not. It is on this basis that they identify evidence of “spare” DNA on the bra-clasp, which may be attributable to contamination.

But do things have to be as strict as they make out? Conti and Vecchiotti give the impression that their approach is generally accepted among DNA analysts. If that’s the case, though, why did the defence experts in the original trial not follow the same line of reasoning?

5. Can the “spare” DNA be accounted for?

It seems an obvious question to ask. If there is additional unexplained DNA on the bra-clasp, can it be associated with any particular individual? There isn’t enough DNA to make a definitive match to anyone, but a fairly good indicative match might be possible. The prosecution would score an enormous point if they are able to tell the court that the additional peaks on the graph are compatible with, say, Kercher’s Italian boyfriend or Knox and Sollecito’s alleged accomplice Rudy Guede. That would mean that the mystery DNA is not evidence of contamination after all, and so the rug would be pulled from under the logic set out in the DNA review.

On the other hand, if it were to emerge that the DNA is compatible with someone from the police’s investigative team (assuming, in the first place, that it is permissible to check from a Human Rights point-of-view), then that would make the contamination thesis seem all the more probable.

  • UPDATE: Since posting, I’ve been able to check the “spare” DNA against Rudy Guede’s profile. There does not appear to be any clear match.

6. How likely is crime scene contamination?

Even if the court is persuaded that contamination – either of the knife, the bra-clasp or both – at the crime scene or in subsequent handing is a possibility to be taken seriously, they may form the view that there were, in reality, no realistic opportunities for such contamination to take place.

The knife was found in a location – Sollecito’s apartment – where Kercher had never been, and so it may seem difficult to imagine how it could have come into contact with her DNA (at least, that is, prior to its arrival at the laboratory, where various samples relating to Kercher had already been tested). The bra-clasp spent a number of weeks lying on the floor in Kercher’s room before it was recovered, so there’s a big window of opportunity for contamination to have taken place. But, again, its not clear how Sollecito’s DNA in particular might have found its way onto the clasp. The amount of his DNA found there is quite large (in fact, it might be argued that this in itself tells against the possibility of contamination), but there does not seem to be good reason to suppose that large quantities of Sollecito’s DNA might have been present in Kercher’s room – a least, not without placing him there at the time she was attacked.

An important job for the prosecution, then, will be to try to convince the court that, from a scientific standpoint, that’s a mistaken way of seeing things. So, they are likely to spend time talking about research suggesting that contamination can be found even in the circumstances in which you would least expect it, and they’ll be hoping that Conti and Vecchiotti and willing to back them up in this regard.

But they will need to strike a fine balance. They need to make the point forcefully, but without appearing to over-egg the pudding.

7. Could DNA be present due to secondary transfer?

“Secondary transfer” is a term used to describe the process of someone transferring someone else’s DNA to a given location. The defence may wish to make the suggestion that this could have happened in either of the cases we are talking about. Either Knox or Sollecito could have had a tiny amount of Kercher’s DNA on their fingertips, for entirely innocent reasons. Either he or she then touched the knife, and the rest is history. Equally, if Kercher had a tiny piece of Sollecito’s DNA on her fingers, it is not hard to see that she might have transferred this herself to her bra.

With respect to the knife, there’s a commonsense reason to be sceptical. Secondary transfers from Kercher were not found elsewhere in Sollecito’s apartment, and it would seem like one hell of an unlucky coincidence if the one place that it had happened was the blade of a knife. But there’s also a scientific reason for scepticism. Research has shown that making a secondary transfer without also transferring large quantities of your own DNA is extremely unlikely. So, if either Knox or Sollecito had transferred Kercher’s DNA to the knife, we would expect to find their DNA mixed into the sample. But it is not there.

The bra-clasp sample, on the other hand, is more compatible with secondary transfer, in that DNA from both the supposed transferor (Kercher) and the supposed transferee (Sollecito) are present. But the problem for the defence in this case is the circumstantial information we have about the sample. We know that someone removed Kercher’s bra after she was attacked. And so, it would seem sensible to suppose that it is at least possible that that person’s DNA might be on her bra-clasp. And what do we find on the clasp..? Bingo! Or so one might think. A key question for the court here is whether the mere possibility of an alternative explanation – let’s face it, there will always be such possibilities – is enough for them to set aside the evidence.

8. What if both of these items of evidence cannot be relied upon?

If the court feels that both the bra-clasp evidence and the knife evidence are unreliable, then the question at the back of their minds will be whether enough evidence remains to uphold the convictions of Knox and Sollecito.

If the report of the assize court is anything to go by, then there quite plainly is. But the appeal court is not necessarily obliged to agree with the lower court on every point. For the defence, it is probably a vain hope that a different conclusion will be reached on every single item of the prosecution case. But how much evidence will be enough?

Most of this evidence isn’t due to get discussed again in court. It will, instead, be discussed by the judges and juror-judges in private. So, whatever happens over the next few sessions, it may be that there is no real indication of what the verdict will be until the moment it is announced.


Knox/Sollecito DNA showdown: an overview (part one)

July 22, 2011

This Monday, 25th July, will be the most significant date so far in the appeal of Amanda Knox and Raffaele Sollecito against their 2009 conviction for the murder of Meredith Kercher. The court in Perugia will begin hearing arguments about two pieces of disputed DNA evidence on which doubt has recently been cast by a review. These arguments are likely to stretch over a number of hearings and travel into the intimate details of DNA analysis and the investigative process in the case. It would be misleading to suggest that we will know the outcome of the appeal just on the basis of this group of hearings. On the other hand, more will rest on the relative strengths of the defence and prosecution arguments in respect of these two pieces of evidence than on anything else that has been, or will be, discussed in court during the appeal process.

The DNA review in a nutshell

Stefano Conti and Carla Vecchiotti of the Sapienza University of Rome were asked by the court to review DNA evidence relating to a knife, allegedly used by Knox to stab Kercher, and the clasp of a bra removed from Kercher’s body after she was attacked.

On the basis of a number of factors, Conti and Vecchiotti take the view that the amount of Kercher’s DNA found in the sample taken from the blade of the knife is so low that it should be classified within a bracket known as Low Copy Number (LCN). This being the case, particularly rigorous procedures should have been applied in the handling of the knife by investigators and during the laboratory analysis of the DNA sample. Conti and Vecchiotti take the view that procedures at the crime scene did not meet these standards. They say they are not able to comment on the general standards in the laboratory, but they note that a number of measures that could have been taken to provide reassurance about the possibility of lab contamination were not.

They looked at two DNA printouts relating to the bra-clasp, one reporting the autosomal DNA of the sample taken from it (i.e. a standard DNA matching test) and one reporting details about the makeup of the y-chromosome content of the DNA. In both of these printouts, they identify peaks alongside those relating to Sollecito and Kercher which, although dismissed in the original testing as noise, they feel ought to be treated as genuine alleles, that is, as representative of real DNA information in the sample. There are a number of possible explanations for the presence of such additional DNA, but the authors of the review suggest that the possibility that these are evidence of low-level contamination of the sample cannot be ruled out. And, if contamination of the sample cannot be ruled out in general, then contamination of the sample with the DNA of Raffaele Sollecito also cannot be ruled out.

Clearly, these findings are good news for the defence. But the big question is how they well they will withstand scrutiny in the courtroom.

In my estimation, at the time the legal teams begin their arguments, the cards will be stacked in favour of the defence with respect to the knife. Specifically in relation to the question of contamination in the lab, the logic of the review is compelling, as I outlined in this post. If the knife is to be kept in play as evidence, then the onus surely falls on the prosecution the show that the risk of contamination was substantially mitigated by the strength of the procedures in place during laboratory analysis.

In contrast, I think the prosecution will walk into the courtroom with the upper hand as far as the bra-clasp is concerned. The court may be impressed by what Conti and Vecchiotti have to say to the extent that it will agree that contamination ought to be taken seriously as a possibility. But, in order to disregard the bra-clasp as evidence, the theoretical possibility of contamination may not be enough. The court will also need to be persuaded that contamination should be seen as plausible in practice, given the facts of the matter. And, in this respect, the review is weaker, appearing to offer only hypothetical and, arguably, not particularly likely-sounding accounts of how it might have taken place. So, a key task for the defence will be to try to paint a more vivid picture of this for the court.

That’s my view. But there are no foregone conclusions here. What I think it might be possible to discern, though, is the nature of the questions that the court will need to get answers to in order to come to a conclusion about these two troublesome pieces of evidence.

Coming up in the next post: key questions for the court


Was Casey Anthony’s DNA on the bra-clasp?

July 20, 2011
DNA readout from bra-clasp in Kercher case

Click on the image for a larger version

In 2009, the journalist Baribie Nadeau mentioned something in an article which many people will have wondered about when they read it. She said that Vincenzo Pascali, a scientific consultant for the prosecution in the early days of the process, had “hinted” that a sample taken from the bra-clasp of the murder victim Meredith Kercher had contained the DNA of not only Raffaele Sollecito but also his alleged accomplice in the crime, Amanda Knox.

It may be thought unlikely that there was much in this. That’s not to impugn Nadeau’s journalism – if a DNA expert hints at something like that then it is worth reporting. At the same time, though, you would think that, if Knox’s DNA really were present on the clasp, the prosecution would have mentioned it by now.

Nevertheless, given the information that is now available about DNA evidence in the case, I thought it would be worth looking into this suggestion.

The first thing to note – and it’s an extremely important thing to note – is that the DNA of Kercher and Sollecito found in the sample from the clasp accounts for either all or very nearly all (depending on which expert you are listening to) of the alleles observed. Since there is so little left to play with, trying to make a further DNA match out of it would seem at bit like looking at a nine and a six and wondering whose phone number in particular they might form part of. Completely impossible, even if you believe that further DNA might be present. Impossible, that is, using any method that is generally considered scientifically reliable.

What you could do, though, is lower your standards and begin to look at peaks that would ordinarily be ignored on the grounds that they could well be nothing more than noise. This makes the peaks that you are including less reliable (how much less reliable depends on how radical you are in including smaller peaks), but it might be argued that there is a legitimate trade-off. If you can get a very good match, then maybe it can be argued that a questionable peak here or there is acceptable. After all, how likely is it that the noise has simply been kind enough to appear in the exact places you would need it to in order to make you incomplete match complete?

So, you can see on the image that I’ve added green dots to the DNA profile taken from the bra-clasp, indicating the places where Knox’s alleles would be expected to be located. And it turns out that it is possible to see a fairly good degree of compatibility with the sample. But I had to go all the way and include even the tiniest bumps on the printout. Because some of these are so small that no numerical information about them is included, I also had to judge a few of the locations by eye (the blue numbers on the image indicate where I did this). This raises the additional problem that my own human error may have some effect on the reliability of what I have done.

But how strong is the actual match? Well, first you have to explain away two things. At loci D8S1179 and D19S433 (the first and tenth groups of peaks on the image), there are small peaks which the DNA review says are above the threshold where we can be confident they are noise. But they are only above the threshold by a hair’s breadth. So maybe we can consider the possibility that they really are noise. Then at locus D7S820 (the third group of peaks in the image), there’s location where you would expect to see an allele relating to Knox, but there is nothing there. Again, maybe this is not so much of a problem. We’re presumably dealing with an extremely faint DNA trace. Maybe it’s simply the case that just one peak out of 29 is so faint as to not be there at all.

What’s starting to emerge, though, is the problem with not having any real standard to go by in terms of which peaks you consider to be real and which you don’t. The judgements you have to make in order to determine whether there is compatibility or not start to become fairly subjective, at least in this case. At each locus point, the ways in which compatibility could arguably be ascertained are numerous, so things are different from how they were in considering the matches to Sollecito and Kercher. Whereas their profiles are quite clear and match 100% to unquestionably genuine alleles on the graph, it seems like you can pretty much see Knox’s DNA profile in the printout according to how much you want to.

A commenter suggested adding dots for a sample known not to be connected to the case. I thought this was a good idea, and whose DNA profile could be more suitable for the task than that of Casey Anthony, recently acquitted of murder in the US? So I’ve added her alleles using pink dots.

I think this goes to further illustrate the problem. Although there are a greater number of problematic spots on the graph that you need to ignore if you want to make Anthony’s DNA fit, some things go the other way. For example, 69% of Knox’s allele’s pair up with peaks on the graph that are above 50 RFU in height (one measure of a potentially genuine allele). It may sound from that like Knox’s DNA is beating the odds. But Anthony’s DNA profile, on the other hand, matches to those >50 RFU peaks 75% of the time. For me, it seems hard to see how you could justify being confident that Knox’s profile is there without also thinking that there is a least a decent chance that Anthony’s could also be there.

Then again, it’s always possible that I have it backwards and that, in reality, the bra-clasp printout offers a new chance for that half of America outraged by Anthony’s aquittal to get her back in court.


Knox/Sollecito: bra-clasp DNA printout

July 18, 2011
Knox/Sollecito bra-clasp printout version 1

Click on the image for a larger version

If you click on the image to the left you’ll see a slightly annotated version of the computer printout for the DNA on the bra-clasp, taken from the review of DNA evidence in the appeal of Amanda Knox and Raffaele Sollecito.

Firstly, I’ve added coloured dots to show the position of alleles relating to Sollecito and to Meredith Kercher.

It should be noted, though, that, while Kercher’s full DNA profile is known, Sollecito’s is not. It is possible to partly work it out, because the review contains details relating to the mixed Kercher/Sollecito sample. According to the Massei report, this sample yielded a match to Sollecito across all 16 of the loci (groups of alleles) tested. Given this knowledge, we can subtract Kercher’s profile from the profile of the mixture, which leaves us with alleles relating to Sollecito.

However, some of Sollecito’s alleles overlap with Kercher’s. I’ve marked these on the image with pale blue dots. It’s unfortunately not possible to be sure which of these are genuine Sollecito alleles, but I’ve also added orange dots for alleles which are common in south Asia and rare in white Europeans (because Kercher’s mother is South Asian, it is likely that these are Kercher’s alleles but not Sollecito’s).

Sorry if anyone’s disappointed not to see a definite Sollecito profile there, but you can console yourself with the knowledge that the probably only reason this would be useful would be for checking the DNA profile on the bra-clasp. And, since using a DNA profile based on the bra-clasp testing in order to check the bra-clasp testing would be a bit circular, you’re not really missing out on much.

Marked with a figure 1 on the image are the peaks which Conti and Vecchiotto, authors of the DNA review, suggest ought to not to be rejected as “stutters” (a type of noise) but instead considered as potentially genuine alleles. I’ll examine this issue further in another post. But, to cut a long story short, Conti and Vecchiotto follow a recommendation in this report that peaks should not be rejected as stutters if they are both over 50 RFU in height and also over 15% of the height of the next known allele to their right.

Hope you like my dots. Just to warn you: for my next trick I propose to add green dots representing the DNA profile of Amanda Knox.


Raffaele Sollecito and the Y-haplotype lottery

July 14, 2011

 Italian lottery ticketIn my last post, I gave my take on what the review of DNA evidence in the Knox/Sollecito appeal said about the alleged murder weapon. The other item they examined is the clasp from Meredith Kercher’s bra, on which, the prosecution claims, Raffaele Sollecito’s DNA was found.

The main issue for the court with regards to the clasp, as with the knife, looks like being the likelihood or otherwise that the DNA results observed might have been the result of contamination. That’s something I’ll look at in my next post.

Before that, I thought it would be a good idea to consider whether there might be any problems with the interpretation of the DNA found on the clasp as belonging to Sollecito. Clearly, if there are then it may be possible to reject the clasp as evidence before even getting to the question of contamination.

Stefano Conti and Carla Vecchiotti, the authors of the review, do raise concerns about the way electronic printouts from the DNA tests were analysed. If you’ve read the review and, particularly, if you’ve only read the conclusion to the review, you might be forgiven for thinking that the match to Sollecito is in some doubt. However, I don’t think this is a correct reading of what has been written, and I don’t think the authors can possibly have intended to leave that impression. I’ll explain why.

Two different sorts of DNA test were run on the sample from the clasp: a test from austosomal DNA (the type of test most people are thinking of when they refer to a “DNA profile”) and a test looking specifically for Y chromosomes.

In each case, Conti and Vecchiotti draw attention to peaks on the graphs that were originally interpreted as “stutters” – small false peaks which are particularly common to find in readings of mixed DNA samples such as this one, where the DNA of the victim was also present. It’s normal practice to just pretend they are not there. The review, though, questions whether all of these peaks really are stutters. They suggest that any peak over 50 RFU might in theory represent a genuine allele, regardless of their size compared to to the “main” peaks observed.

With regard to the tests run to identify Y-chromosomes in the sample, the review agrees with the finding of compatibility between the sample and Sollecito’s Y haplotype. You can see how this is difficult to deny by looking at page 129 of the review. At each locus point in the computer printout (i.e. each group of peaks you can see), the largest of the peaks corresponds perfectly in each case to Sollecito’s profile.

What the review is suggesting here is not that there is any doubt about that, but that some of the smaller peaks which are above 50 RFU might not be stutters. Instead, they may point to the presence of an additional Y-chromosome or chromosomes other than Sollecito’s. This, in turn, calls into question a working hypothesis of police scientist Patrizia Stefanoni in the original tests: that the DNA she was looking at represented a mixture of the victim plus one other person. I’ll examine the potential implications of this in my next post.

In her autosomal DNA testing of the sample from the clasp, Stefanoni found a match with Sollecito over 16 locus-points. That’s a very strong finding.

To give you an idea of how strong, I’ve done my own calculation. For each locus, I looked up the population frequencies for the relevant alleles (using the highest value present relating to Italy) in this database. Because some of these are overlaps with Kercher’s profile (i.e. they would be present even if Sollecito’s DNA were not) I then erred very much on the safe side and gave them a dummy frequency of 1. I then used the numbers to calculate the genotype frequency for each locus (slightly tedious to explain how that is done – please let me know if you care).

All you then need to do to get an overall frequency (or “random match probability”) for the 16 loci is multiply all the genotype frequencies together and invert the result (i.e. divide one by it).

I’ve either explained all that clearly or I haven’t. In either case, what I came up with was a random match probability of one in about six thousand billion.

I’m not a DNA expert. This is a very rough estimate and there may be methodological issues with my calculation. For example, maybe it would be better to use worldwide frequency figures rather than just concentrating on Italy. But the real point is not the specific figure I came up with, just the fact that is is very, very large. Genotype frequency values tend to be lower than 0.3. So, whatever specific values you use, once you’ve multiplied a load of them together and then inverted, you are guaranteed to end up with a very large number.

The specific problem identified in the review is that at four of the locus points there are peaks present which were disregarded as a stutter in the original testing, but which could be considered genuine peaks, according to Conti and Vecchiotti. You can get an idea of what they are talking about from page 120 of the review. The large peaks seen here are those that match with the victim. The others are, according to Stefanoni, a mixture of stutters and matches to Sollecito.

If we accept the possibility that some of the stutters may be real peaks, then this may have an effect on the random match probability.

There may be a number of potential ways of attempting to account for this. But, even if we were to bend over backwards for the defence and scrap the affected loci altogether, we would still have an overall frequency of one in about 22 billion over the 12 remaining loci. That slashes the odds quite considerably, but it still doesn’t exactly result in a small number.

Now, you might be tempted to formulate a line of thinking, based on the idea that those ambiguous stutters/peaks might represent some unknown person or persons, that perhaps the DNA reading which looks like it matches Sollecito is actually a random combination of DNA from other people. The trouble is, though, that this proposition doesn’t make any difference to the maths. What we’re talking about is just the frequency (to all intents and purposes, the probability) of that particular combination of alleles occurring in sequence. How they got there doesn’t really matter, to the extent that there’s just no realistic statistical possibility that they represent anything other than Sollecito’s DNA.

Still not convinced? Okay, well consider the Y-haplotype DNA. That’s a perfect match over 17 loci. A Y-haplotype match is generally not held to be usable for identification simply because it is not unique. Your Y-chromosome (if you have one) is, barring random mutations, likely to be shared with your father and other Y-chromosomed members of your immediate family. Or, if your Y-haplotype is a very common one, your not-so-immediate family. It’s not impossible that you have exactly the same Y-chromosome as hundreds of thousands of other people. Or it might be a handful. But, without knowing which it is, your Y-chromosome can’t be used to identify you.

Unfortunately, it also seems that available data isn’t extensive enough to reliably assign a population frequency to Y-haplotype. However, it is possible to classify a Y-haplotype as “rare”. At the original trial, Stefanoni referred to having checked Sollecito’s Y-haplotype in something called the YRHD database. You can do this yourself if you want. The search form is here and Sollecito’s Y-haplotype reading is on page 130 of the review. What you’ll find is that, out of 36,477 Y-haplotypes in the database, none match Sollecito’s.

[Note: I redid this search in April 2013, by which time the database had grown to 112,005 Y-haplotypes, but there was still no match for Sollecito.]

I’m thinking of the Y-haplotype as being like the bonus number in a lottery game. It’s not worth much as an identifier on its own, but it’s priceless if you’ve already matched all the main numbers.

NOTE: This post originally contained some incorrect figures and has now been corrected.


Knox/Sollectio: was the knife contaminated?

July 9, 2011
The Qubit Fluorometer

The Qubit Fluorometer, used in DNA analysis relating to the alleged murder weapon

One of the two exhibits in the trial of Amanda Knox and Raffaele Sollecito to be looked at by Stefano Conti and Carla Vecchiotti as part of their review of DNA evidence in the case is a knife, recovered from Sollecito’s flat and alleged by prosecutors to have been used by Knox to stab Meredith Kercher in the neck.

Conti and Vecchotti agree with the opinion of the chief police scientist, Patrizia Stefanoni, that Knox’s DNA was present on the handle of the knife and they don’t dispute the match between the DNA found on the blade and that of the victim. But they raise clear concerns that the DNA profile observed in relation to the blade could have been the result of contamination.

The reasoning behind this turns on their characterisation of the the DNA sample from the blade as “Low Copy Number” (LCN), essentially meaning that there were so few examples of the DNA in question within the sample that, according to mainstream scientific opinion, special measures would have been required so as to ensure the integrity of the testing.

In her trial testimony, Stefanoni appeared to accept the proposition that the sample in question may indeed have been an LCN sample. It appears difficult to be absolutely sure about this, because there is no accurate record of the quantity of originating material (Stefanoni has said it was “in the order of a few hundred picograms (pg)”). Quantifications during a process known as qPCR, it seems, would have given a strong indication, but there is no record of these having been performed – perhaps because of the very fact that the sample was so small as to be out of the range of sensitivity offered by the equipment that would have been used.

However, the review highlights two reasons to suppose that the sample must have been of an LCN-type quantity. Firstly, there are what are known as “peak imbalances” in the graphical representations of the DNA which were produced. In most graphical printouts of DNA tests, peaks come in pairs. In an imaginary perfect test, the pairs would all be of equal height to one another. That is rarely the case in practice, so a ratio of 3:5 is normally considered acceptable. But, it can be seen from the graphs reproduced from page 68 on in the review that some of the pairings are more imbalanced than that. Although these imbalances can be produced by a number of means, they can be indicative of the presence of LCN material, so this provides some support for the notion that we are dealing with LCN. Moreover, if you accept that the raw material was “a few hundred picograms” and note that the volume of the solution from which the DNA reading was obtained was 10 microlitres (μl), then it follows that the concentration of that solutions must have been a few tens of pg/μl. According to the review, 200 pg/μl is generally considered to be a threshold below which material should be treated as LCN.

One difficulty with analysing an LCN sample is that, because its presence in a solution is so faint, amplification is required during the PCR process (indeed, it seems clear that Stefanoni did carry out amplification on the sample). Think about this as being like turning up the volume on a cassette player to hear something that has been recorded at a very low volume. Inevitably you are also turning up the hiss. Background noise will normally be easy enough to distinguish from the genuine data, but the real problem is that, as you amplify, you may be amplifying faint traces of contamination that are also present. So, in our case, if there is a reasonable risk that Meredith Kercher’s DNA might have been present as a trace-level contaminant, then the test conducted ought not to be considered reliable.

Conti and Vecchiotti portray this a real risk that could have arisen at any stage of the investigative process, from the recovery of the knife through to the final tests in the lab. They point to a body of scientific literature recommended specific procedures, above what may typically be implemented, in order to minimise the risk of contamination in the recovery, handling and analysis of the evidence, and question whether such procedures were applied in the Kercher case. It is even suggested that the sample from the blade should have been tested in an entirely different laboratory.

I think the strength of this argument varies according to the context you are talking about. Failure to protect against contamination is not necessarily to be excused at any stage. But, from the point-of-view of the results we are considering, it only really matters if there is an appreciable risk that the data observed could have resulted from contamination. So, it should be considered that the location from which the knife was recovered – Sollecito’s flat – is not one where the victim’s DNA would be expected to be present, because it is somewhere where she had never set foot. Regardless of how suitable the procedures carried out there were, there does not seem to be a real risk of contamination.

Similarly, in between the flat and the lab, the knife does not appear to have been in any location where Kercher’s DNA might be supposed to have been present nor handled by anyone who had been in contact with Kercher’s DNA.

As a side note, the review suggests that secondary contamination can never be ruled out in DNA testing, points to an authority that detecting this type of contamination is more likely where LCN is concerned. For example, perhaps Sollecito shook hands with Kercher at some point, then carried her DNA back to his flat and contaminated the knife. In theory, it is probably correct to say that this possibility cannot be ruled out. But the prosecution may be expected to argue that this type of contamination is an ever-present and merely theoretical risk. What the court ought to want to ascertain is exactly how likely such contamination is.

Even if it might be argued that contamination from Kercher’s DNA at Sollecito’s flat or during the initial handling of the evidence is a remote possibility, it is certain that her DNA was present in the lab. At least 50 samples containing it were tested there, 20 or more of them prior to the testing of the knife.

For this reason, a key question for the court is whether the procedures in the lab were adequate for minimising the risk of cross-contamination of samples by the people working there, particularly given the apparent likelihood that the material in question was an LCN sample. The authors of the review don’t categorically say that they weren’t, but that they don’t have enough information to make a judgement. The court at the original Knox/Sollecito trial was satisfied that the standards of the laboratory were adequate in this respect. Will the appeal court take the same view? Will it feel obliged to hold the police scientists to higher standards in light of the review?

If the procedures in place (an actually implemented) in the lab are found to satisfactory, that is not necessarily all there is to it. There are checks on contamination that can be carried out but were not in this case, perhaps in part owing to the small quantity of material being studied.

Ideally, as was conceded by Stefanoni in the original trial, the sample should have been broken into two or more portions to be tested separately. Assuming that similar results would have been replicated on at least two occasions, this would have shown contamination to be less likely.

As a further precaution, the presence of some type of organic material might have been established. Now, it may be felt that the victim’s DNA is the victims DNA. What does it matter whether it came from blood, or skin or whatever? However, if the presence of some particular type of cell were known, then this would provide an indication against the idea that the results were contamination. Stefanoni seems to have performed a test for blood which was negative, and then proceeded on the basis that the sample was too small for the test to have worked properly.

It seems likely that dividing the sample simply wasn’t possible and, although Stefanoni may now wish that she had been more thorough in determining the biological nature of the material she was dealing with, that lapse is probably not enough in itself to invalidate her results.

A bigger problem to my understanding (although the review doesn’t stress it in the way I might have expected) is the issue of how control tests were performed. Standard procedure is to run negative controls, where the test is performed on a saline solution or something else not expected to contain any DNA, so as to check for the presence of contamination already present in the equipment or tube. A positive control should also be run, on a sample whose properties are known, in order to check that the equipment is behaving as it would be expected to (a bit like checking your bathroom scales using a bag of sugar).

These control tests should really be performed not only at the start of testing for each sample, but also when an amplification is performed on a sample. This is particularly important for the negative control, because of the possibility that the amplification will reveal contamination that may not be evident prior to the amplification. But Conti and Vecchiotti report that they see no evidence that this was done. Perhaps the bench will be satisfied if Stefanoni performed the controls without saving them electronically and is able to confirm that no problems were observed. But there’s a clear problem here for the prosecution if it emerges that the controls were not performed.

The most important things for discussion at the next hearing on 25 July will, I think, be the quality of the procedures in place in the police lab for reducing the risk of cross-contamination between samples and the issue of whether or not adequate controls were performed on the knife-blade sample. The reliability of the knife as a piece of evidence in the case really relies on those two things going in the favour of the prosecution.


What makes Amanda Knox dance?

July 7, 2011

According to one media report, Amanda Knox literally danced for joy last week on hearing of the conclusions of the independent review of DNA evidence which helped to convict her and Raffaele Sollecito of the 2007 murder of Meredith Kercher. There’s always reason to be cautious when you encounter an image like that in newspaper report. After all, in all probability, it’s been transcribed during a phonecall with Knox’s PR people. But, in this case, if it isn’t true then it might as well be, I think. It’s hard to imagine that Knox has received better news lately.

Knox and Sollecito’s appeal hasn’t been great for them so far. Nothing so far heard in court seems likely to have swayed the judges and juror-judges in their favour. Witness testimony and courtroom discussions have been so tangential to the central thread of evidence in the case that you might be forgiven for wondering if the defence actually set out with a plan to emphasise their lack of anything significant to bring to proceedings.

But the DNA review is different. Stefano Conti and Carla Vecchiotti of the Sapienza University of Rome were asked by the court to look at the DNA evidence relating to two trial exhibits of particular importance. The first was a knife, alleged by prosecutors to have been used by Amanda Knox to stab Meredith Kercher. Second was the clasp of Kercher’s bra, on which prosecutors allege Sollecito left his DNA as he removed the bra following the murder.

In fairly clear terms, Conti and Vecchitotti raise concerns about the reliability of DNA evidence relating to both of these exhibits. Over the next few posts, I’m planning to do my best to explain what those concerns are and what, if anything, the prosecution might be able to say in response.

Before I do that, though, a few things to bear in mind if you are not familiar with the workings of the case. There can be little doubt that the results of the review are as good as could have realistically been hoped for by the defence. However, the review is not definitive. It is a report prepared for the court to consider. They can’t very well ignore it, but they don’t have to accept it at face value. Given that it is favourable to the defence, the thing that will really determine its impact is the strength of the counter-arguments that prosecutors and the lawyer for the Kercher family will inevitably put during the next hearing on 25 July, and how convincingly those counter-arguments come across.

Another thing to understand is that, although a less favourable review may well have spelled the end for the defence case, the converse it not true. The prosecution case is made up of a number of evidentiary planks. The review threatens one of these, but nothing so far in the appeal has very seriously undermined the others. If the judges accept the findings of the review, then the question is: will they fell able to step on the remaining planks and cross the floor?

For the sake of ensuring the firm foundations of their eventual decision, they will probably want to simply accept or reject each element in the review and act accordingly by either accepting or rejecting the relevant DNA evidence. However, prosecutors are likely to want to encourage them down an alternative path. So long as they don’t allow their decision to hang by evidence that is questioned in the review, they could reasonably decide instead to attempt to quantify the degree if unreliability of each piece of evidence. Is it unreliable to the extent of being meaningless? Or does it have value as circumstantial evidence as being reliable on a balance of probabilities? In that case, we might be dealing with a plank that is not absent, but one which you wouldn’t want to step on too hard.

So, all that said, the question is whether the review makes it likely that Amanda Knox will be dancing a freedom waltz come the autumn. Well, the review is fairly linear in its approach, with the authors giving their opinion on what the court asked them to look at, and not really fully nailing-down the issues by considering different perspectives. They probably don’t take that to be their job. Francesco Maresca, lawyer for thee Kercher family, seems to disagree with that, wondering how such an unequivocal report can be appropriate. You can understand him frustration. Surely it is not too much to expect that the counter-arguments put by the prosecution in the original trial might have been considered, even if only for the purpose of explaining why they are wrong. But maybe Maresca can see a potential silver lining to this. At least it should give him and his colleagues space to focus on these counter-arguments at the all-important 25 July hearing. This could have been all about what is wrong with the DNA evidence, but they have the opportunity to make it as much about what is wrong with the review.

But, make no mistake, it isn’t going to be a cakewalk for them. In my next post, I’m going to try to give an idea of the kind of footwork they’ll need to master in order to deal with what the review has to say about the alleged murder-weapon in the case, a knife recovered by police at the Raffale’s Sollecuto’s flat.


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